Merge branch 'master' into programmers-docs

Author: robertodr

.github/workflows/build-test.yml

@@ -21,6 +21,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        # setup-miniconda not compatible with macos-latest presently.
+        # https://github.com/conda-incubator/setup-miniconda/issues/344
         os: [ubuntu-latest, macos-12]
 
     steps:
@@ -35,7 +37,7 @@ jobs:
         key:
           ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/mrchem-gha.yml') }}
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
           auto-update-conda: true
           auto-activate-base: false

CMakeLists.txt

@@ -58,6 +58,8 @@ include(${PROJECT_SOURCE_DIR}/cmake/downloaded/autocmake_code_coverage.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/mpi.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/omp.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/sad_basis.cmake)
+include(${PROJECT_SOURCE_DIR}/cmake/custom/hirshfeld.cmake)
+include(${PROJECT_SOURCE_DIR}/cmake/custom/azora_potentials.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/main.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/feature_summary.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/tests.cmake)

README.md

@@ -14,7 +14,6 @@ chemistry (Hartree-Fock and Density Functional Theory).
 The code is being developed at the Hylleraas Centre for Quantum Molecular
 Sciences at UiT - The Arctic University of Norway.
 
-### User support: [mrchem.slack.com](https://join.slack.com/t/mrchem/shared_invite/enQtNTI3MjMzNjM0NTk0LWNkODZjNTMwYmM4NmRmODExMjQzMDc3NThlMzNmNmIyNWQwM2YwOGY0OWY4NmNmNzE4ZmM2NzgxYzUzNDg3NDM)
 ### Documentation: [mrchem.readthedocs.io](http://mrchem.readthedocs.io)
 
 

cmake/custom/azora_potentials.cmake

@@ -0,0 +1,7 @@
+set(AZORA_POTENTIALS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/azora_potentials CACHE STRING "Path to azora potentials")
+set(AZORA_POTENTIALS_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/azora_potentials)
+install(
+  DIRECTORY share/azora_potentials
+  DESTINATION share/${PROJECT_NAME}
+  )
+

cmake/custom/hirshfeld.cmake

@@ -0,0 +1,7 @@
+
+set(HIRSHFELD_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/hirshfeld CACHE STRING "Path to azora potentials")
+set(HIRSHFELD_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/hirshfeld)
+install(
+  DIRECTORY share/hirshfeld
+  DESTINATION share/${PROJECT_NAME}
+  )

doc/users/schema_input.json

@@ -101,6 +101,7 @@
       "zeta": int,                           # Zeta quality for AO basis
       "method": string,                      # Name of method for initial energy
       "localize": bool,                      # Use localized orbitals
+      "rotate": bool,                        # Rotate orbitals in initial guess
       "restricted": bool,                    # Use spin restricted orbitals
       "relativity": string,                  # Name of relativistic method
       "screen": float,                       # Screening used in GTO evaluations

doc/users/user_inp.rst

@@ -449,6 +449,7 @@ The ``core`` and ``sad`` guesses are fully specified with the following keywords
       guess_prec = 1.0e-3                   # Numerical precision used in guess
       guess_type = sad_gto                  # Type of inital guess (chk, mw, cube, core_XX, sad_XX)
       guess_screen = 12.0                   # Number of StdDev before a GTO is set to zero (sad_gto)
+      guess_rotate = true                   # Localize/Diagonalize guess orbitals before calculating the initial guess energy
     }
 
 Checkpointing

doc/users/user_ref.rst

@@ -231,13 +231,13 @@ User input reference
 
     **Default** ``-1``
 
-   :omp_threads: Force the number of OpenMP threads.
-
+   :omp_threads: Force the number of omp threads (leave default is better). 
+  
     **Type** ``int``
-
+  
     **Default** ``-1``
-
-    :Basis: Define polynomial basis. 
+  
+ :Basis: Define polynomial basis. 
 
   :red:`Keywords`
    :order: Polynomial order of multiwavelet basis. Negative value means it will be set automatically based on the world precision. 
@@ -326,14 +326,14 @@ User input reference
 
     **Default** ``True``
 
-   :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). 
+   :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). ``azora`` uses atomic ZORA potentials, which are precomputed and read from the directory  specified in the ``azora_potential_path`` keyword. 
 
     **Type** ``str``
 
     **Default** ``none``
 
     **Predicates**
-      - ``value.lower() in ['none', 'zora', 'nzora']``
+      - ``value.lower() in ['none', 'zora', 'nzora', 'azora']``
 
    :environment: Set method for treatment of environment. ``none`` for vacuum calculation. ``PCM`` for Polarizable Continuum Model, which will activate the ``PCM`` input section for further parametrization options. The ``PB`` and ``LPB`` variants add the Poisson-Boltzmann and Linearized Poisson-Boltzmann solvers, respectively. 
 
@@ -374,6 +374,12 @@ User input reference
 
     **Default** ``True``
 
+   :azora_potential_path: Path to the directory containing the AZORA potentials. If not specified, the default potentials will be used. Look into the readme file in the share/azora_potentials directory for information about the potential file format. 
+  
+    **Type** ``str``
+  
+    **Default** ``none``
+  
  :DFT: Define the exchange-correlation functional in case of DFT. 
 
   :red:`Keywords`
@@ -440,12 +446,45 @@ User input reference
 
     **Default** ``[]``
 
+   :hirshfeld_charges: Compute Hirshfeld charges. 
+  
+    **Type** ``bool``
+  
+    **Default** ``False``
+  
    :geometric_derivative: Compute geometric derivative. 
 
     **Type** ``bool``
 
     **Default** ``user['GeometryOptimizer']['run']``
 
+ :Forces: Define parameters for the computation of forces. 
+
+  :red:`Keywords`
+   :method: Method for computing forces. ``surface_integrals`` (more accurate) uses surface integrals over the quantum mechanical stress tensor, while ``hellmann_feynman`` uses the Hellmann-Feynman theorem. 
+  
+    **Type** ``str``
+  
+    **Default** ``surface_integrals``
+  
+    **Predicates**
+      - ``value.lower() in ['surface_integrals', 'hellmann_feynman']``
+  
+   :surface_integral_precision: Precision of the surface integrals used in the computation of forces. Determines the number of Lebedev grid points used in the surface integration. 
+  
+    **Type** ``str``
+  
+    **Default** ``medium``
+  
+    **Predicates**
+      - ``value.lower() in ['low', 'medium', 'high']``
+  
+   :radius_factor: Sets the radius of the surface used in the computation of forces. The radius is given by this factor times the distance to the neariest neighbour. Must be between 0.1 and 0.9. This should rarely need to be changed. Different values can change the accuracy of the forces. 
+  
+    **Type** ``float``
+  
+    **Default** ``0.5``
+  
  :ExternalFields: Define external electromagnetic fields. 
 
   :red:`Keywords`
@@ -722,6 +761,12 @@ User input reference
     **Predicates**
       - ``value[-1] != '/'``
 
+   :guess_rotate: Localize/Diagonalize the initial guess orbitals before calculating the initial guess energy. 
+  
+    **Type** ``bool``
+  
+    **Default** ``True``
+  
    :write_orbitals: Write final orbitals to disk, file name ``<path_orbitals>/phi_<p/a/b>_scf_idx_<0..Np/Na/Nb>``. Can be used as ``mw`` initial guess in subsequent calculations. 
 
     **Type** ``bool``

python/README.md

@@ -12,6 +12,7 @@ To run the script:
 
 ```bash
 $ cd python/mrchem
+$ rm -r input_parser/plumbing/pyparsing
 $ python update_input_parser.py
 ```
 
@@ -24,7 +25,7 @@ This does three things:
 Each of these steps can be deactivated by appropriate flags. For help on running the script, run
 
 ```bash
-$ cd python
+$ cd python/mrchem
 $ python update_input_parser.py -h
 ```
 
@@ -33,7 +34,8 @@ If the `Constants` and `Elements` input sections are unchanged, you can update t
 The utility script can also do this, by specifying the flag `--skip-template`:
 
 ```bash
-$ cd python
+$ cd python/mrchem
+$ rm -r input_parser/plumbing/pyparing
 $ python update_input_parser --skip-template
 ```
 
@@ -43,6 +45,7 @@ You can also perform these steps manually without using the utility script:
 
 ```bash
 $ cd python
+$ rm -r mrchem/input_parser/plumbing/pyparsing
 $ parselglossy generate --template template.yml --docfile user_ref.rst --doc-header="User input reference" --target="mrchem/input_parser"
 $ cp mrchem/input_parser/docs/user_ref.rst ../doc/users/user_ref.rst
 ```

python/mrchem/helpers.py

@@ -59,7 +59,19 @@ def write_scf_fock(user_dict, wf_dict, origin):
             "include_nuclear": user_dict["ZORA"]["include_nuclear"],
             "include_coulomb": user_dict["ZORA"]["include_coulomb"],
             "include_xc": user_dict["ZORA"]["include_xc"],
+            "isAZORA": False,
+            "azora_potential_path": user_dict["ZORA"]["azora_potential_path"]
         }
+    # AZORA
+    if user_dict["WaveFunction"]["relativity"].lower() == "azora":
+        fock_dict["zora_operator"] = {
+            "include_nuclear": False,
+            "include_coulomb": False,
+            "include_xc": False,
+            "isAZORA": True
+        }
+        if user_dict["ZORA"]["azora_potential_path"].lower() != "none":
+            fock_dict["zora_operator"]["azora_potential_path"] = user_dict["ZORA"]["azora_potential_path"]
 
     # Kinetic
     fock_dict["kinetic_operator"] = {"derivative": user_dict["Derivatives"]["kinetic"]}
@@ -224,6 +236,7 @@ def write_scf_guess(user_dict, wf_dict):
         "external_field": wf_dict["external_name"],
         "screen": scf_dict["guess_screen"],
         "localize": scf_dict["localize"],
+        "rotate": scf_dict["guess_rotate"],
         "restricted": user_dict["WaveFunction"]["restricted"],
         "file_chk": f"{scf_dict['path_checkpoint']}/phi_scf",
         "file_basis": file_dict["guess_basis"],
@@ -274,7 +287,7 @@ def write_scf_solver(user_dict, wf_dict):
 def write_scf_properties(user_dict, origin):
     prop_dict = {}
     if user_dict["Properties"]["dipole_moment"]:
-        prop_dict["dipole_moment"] = {}
+        prop_dict["dipole_moment"] = {} 
         prop_dict["dipole_moment"]["dip-1"] = {
             "operator": "h_e_dip",
             "precision": user_dict["world_prec"],
@@ -293,7 +306,16 @@ def write_scf_properties(user_dict, origin):
             "operator": "h_nuc_grad",
             "precision": user_dict["world_prec"],
             "smoothing": user_dict["Precisions"]["nuclear_prec"],
+            "method": user_dict["Forces"]["method"],
+            "surface_integral_precision": user_dict["Forces"]["surface_integral_precision"],
+            "radius_factor": user_dict["Forces"]["radius_factor"],
+        }
+    if user_dict["Properties"]["hirshfeld_charges"]:
+        prop_dict["hirshfeld_charges"] = {}
+        prop_dict["hirshfeld_charges"]["hirshfeld-1"] = {
+            'precision': user_dict["world_prec"]
         }
+
     return prop_dict
 
 
@@ -506,12 +528,21 @@ def parse_wf_method(user_dict):
 
     # Determine relativity name label for print outs to the output file
     relativity_name = "None"
+    wf_dict = dict()
     if user_dict["WaveFunction"]["relativity"].lower() in ["none"]:
         user_dict["WaveFunction"]["relativity"] = "off"
         user_dict["ZORA"]["include_nuclear"] = False
         user_dict["ZORA"]["include_coulomb"] = False
         user_dict["ZORA"]["include_xc"] = False
 
+    if user_dict["WaveFunction"]["relativity"].lower() in ["azora"]:
+        relativity_name = "AZORA"
+        user_dict["WaveFunction"]["relativity"] = "azora"
+        user_dict["ZORA"]["include_nuclear"] = False
+        user_dict["ZORA"]["include_coulomb"] = False
+        user_dict["ZORA"]["include_xc"] = False
+        user_dict["ZORA"]["isAZORA"] = True
+
     if user_dict["WaveFunction"]["relativity"].lower() in ["nzora"]:
         user_dict["WaveFunction"]["relativity"] = "zora"
         user_dict["ZORA"]["include_nuclear"] = True
@@ -534,10 +565,10 @@ def parse_wf_method(user_dict):
         else:
             raise RuntimeError("ZORA selected, but no ZORA potential included")
 
-        if user_dict["ZORA"]["include_xc"] and not restricted:
-            raise RuntimeError(
-                "ZORA (V_xc) not available for unrestricted wavefunctions"
-            )
+        # if user_dict["ZORA"]["include_xc"] and not restricted:
+        #     raise RuntimeError(
+        #         "ZORA (V_xc) not available for unrestricted wavefunctions"
+        #     )
 
     # Determine environment name label for print outs to the output file
     environment_name = "None"
@@ -560,14 +591,12 @@ def parse_wf_method(user_dict):
         # Labels to aggregate
         external_name = f"Electric field ({x}, {y}, {z})"
 
-    wf_dict = {
-        "relativity_name": relativity_name,
-        "environment_name": environment_name,
-        "external_name": external_name,
-        "method_name": method_name,
-        "method_type": method_type,
-        "dft_funcs": dft_funcs,
-    }
+    wf_dict["relativity_name"] = relativity_name
+    wf_dict["environment_name"] = environment_name
+    wf_dict["external_name"] = external_name
+    wf_dict["method_name"] = method_name
+    wf_dict["method_type"] = method_type
+    wf_dict["dft_funcs"] = dft_funcs
     return wf_dict
 
 

python/mrchem/input_parser/README.md

@@ -1,2 +1,2 @@
-This file was automatically generated by parselglossy on 2024-01-29
+This file was automatically generated by parselglossy on 2024-08-15
 Editing is *STRONGLY DISCOURAGED*

python/mrchem/input_parser/__init__.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2024-01-29
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*